Yesterday, I released a new utility called vcromclaim. Its primary purpose is to extract ROMs from Virtual Console games on NAND dumps created by BootMii and other NAND dumpers. It also extracts manuals and some game saves as an added bonus.

The ROMs and saves it outputs are compatible with popular emulators. The manuals are HTML files. It can decompress virtually any compressed file it encounters.

At present, it works almost flawlessly with the following VC platforms:

Another huge feature: vcromclaim automatically restores the sound to VC SNES games where the original ROM with correct sound is not included. To my knowledge, there is no other software in existence that can do this - I reverse engineered it myself.

I don't think it's possible to use the emulator itself (main.dol, I suppose) on a WAD, since it reads data from the disc and not from the NAND. Most of ppl want this because of its compatibility with WiiMotes. Sorry if I misunderstood your question.